Version Compatibility

Reference examples tested with: R stats (base), clusterProfiler 4.10+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

KEGG Pathway Enrichment

Core Pattern

Goal: Identify KEGG metabolic and signaling pathways over-represented in a gene list.

Approach: Test for enrichment using the hypergeometric test via clusterProfiler enrichKEGG against the KEGG online database.

"Find enriched KEGG pathways in my gene list" → Test whether KEGG pathway gene sets are over-represented among significant genes.